diff --git a/README.md b/README.md index 709c86d..011023e 100644 --- a/README.md +++ b/README.md @@ -114,7 +114,7 @@ Singularity Image The easiest way to run GALBA is using singuarlity. We provide a docker container to build a singularity image (tested with singularity version 3.10.0-dirty). **We only include Miniprot in Docker & Singularity!** GenomeThreader is not included. -Build as follows (requires 1.2 GB disk space): +Build as follows (requires 1.4 GB disk space): ``` singularity build galba.sif docker://katharinahoff/galba-notebook:latest @@ -126,23 +126,6 @@ Execute GALBA from galba.sif like this (i.e. it automatically mounts the user's singularity exec galba.sif galba.pl ``` -Known issue with partitionLargeSeqeunces or partitionLargeSequences -------------------------------------------------------------------- - -The AUGUSTUS developers team is currenlty transitioning between versions. One (very minor) change in Augustus is that we fixed a typo in the term "partionLargeSeqeunces (which is now of course partitionLargeSequences). It is a Pygustus argument. Pygustus looks for possible arguments in two places: if there is no json file with the required parameters in the $AUGUSTUS_CONFIG_PATH/parameters, then it uses its own (typo-fixed) json file. If it does find the json file in the $AUGUSTUS_CONFIG_PATH/parameters folder, then it uses that file, and it depends on what age that file has on your system whether our latest-tagged image will work, or not. The latest-tagged image will work for the older (mis-spelled) json file. - -If the image built from docker://katharinahoff/galba-notebook:latest dies at pygustus execution, please build the image from a different tag: - -``` -singularity build galba.sif docker://katharinahoff/galba-notebook:pygustusbug -``` - -and then try execution, again. - -In general, the tag docker://katharinahoff/galba-notebook:pygustusbug will probably work on all systems that do not have an older json file in the $AUGUSTUS_CONFIG_PATH/parameters folder. - -We will try to put some safeguards into the galba.pl code, later. Right now, you need to simply test which of the two tags works for your system. - Running GALBA in Singularity outside of $HOME --------------------------------------------- diff --git a/scripts/galba.pl b/scripts/galba.pl index 1396e44..14ee7c6 100755 --- a/scripts/galba.pl +++ b/scripts/galba.pl @@ -1155,7 +1155,7 @@ sub set_AUGUSTUS_BIN_PATH { } } - if ( not( defined($AUGUSTUS_BIN_PATH) ) ) { + if( not( defined($AUGUSTUS_BIN_PATH) ) ) { my $aug_bin_err; $aug_bin_err .= "There are 3 alternative ways to set this variable for\n" @@ -1177,7 +1177,7 @@ sub set_AUGUSTUS_BIN_PATH { . " executable that is available in your \$PATH\n" . " (in this case, the augustus executable is not available).\n"; $prtStr = "\# " . (localtime) . ": ERROR: in file " . __FILE__ - . " at line ". __LINE__ . "\n" . "\$AUGUSTUS_BIN_PATH not set!\n"; + . " at line ". __LINE__ . "\n\$AUGUSTUS_BIN_PATH not set!\n"; $logString .= $prtStr; $logString .= $aug_bin_err if ($v > 0); print STDERR $logString; @@ -3323,7 +3323,7 @@ sub make_prot_hints { } # Currently running miniprot twice, the first run only serves training gene generation $cmdString - .= "$prot_aligner -ut$CPU --outn=1 --gtf $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $alignment_outfile "; + .= "$prot_aligner -ut$CPU --outn=1 --gtf $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $alignment_outfile 2>> $errorfile"; print LOG "\# " . (localtime) . ": running Miniprot to produce protein to " @@ -3460,7 +3460,7 @@ sub make_prot_hints { # Currently running miniprot twice, the first run only serves training gene generation, the second shall produce the actual hints $cmdString - .= "$prot_aligner -ut$CPU --outn=1 --aln $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $miniprot_aln_file "; + .= "$prot_aligner -ut$CPU --outn=1 --aln $otherfilesDir/genome.mpi $prot_seq_files[$i] >> $miniprot_aln_file 2>> $errorfile"; print LOG "\# " . (localtime) . ": running Miniprot to produce protein to "